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- PDB-5nmx: Crystal Structure of the pyrrolizidine alkaloid N-oxygenase from ... -

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Basic information

Entry
Database: PDB / ID: 5nmx
TitleCrystal Structure of the pyrrolizidine alkaloid N-oxygenase from Zonocerus variegatus in complex with FAD and NADP+
ComponentsFlavin-containing monooxygenase
KeywordsOXIDOREDUCTASE / pyrrolizidine alkaloid N-oxygenase / flavin-containing monooxygenase / rossmann fold / FAD / NADP / two dinucleotide binding domain flavoprotein / senecionine
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / Oxidoreductases / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin-containing monooxygenase
Similarity search - Component
Biological speciesZonocerus variegatus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsScheidig, A. / Kubitza, C. / Faust, A. / Ober, D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus.
Authors: Kubitza, C. / Faust, A. / Gutt, M. / Gath, L. / Ober, D. / Scheidig, A.J.
History
DepositionApr 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-containing monooxygenase
B: Flavin-containing monooxygenase
C: Flavin-containing monooxygenase
D: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38515
Polymers197,1964
Non-polymers6,18911
Water28,3201572
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C: Flavin-containing monooxygenase
hetero molecules

A: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6807
Polymers98,5982
Non-polymers3,0825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
B: Flavin-containing monooxygenase
hetero molecules

D: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7058
Polymers98,5982
Non-polymers3,1076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Unit cell
Length a, b, c (Å)74.076, 76.082, 81.669
Angle α, β, γ (deg.)71.810, 81.640, 82.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Flavin-containing monooxygenase


Mass: 49299.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zonocerus variegatus (insect) / Gene: pno / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0N8S9, Oxidoreductases
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: TRIS-HCl, MgCl2, PEG3350, NADP+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→77.13 Å / Num. obs: 213235 / % possible obs: 96.1 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 39.3
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) all: 2.3 / % possible all: 47.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xve

2xve


Resolution: 1.6→77.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1974 / WRfactor Rwork: 0.1704 / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8716 / SU B: 0.002 / SU ML: 0 / SU R Cruickshank DPI: 0.0787 / SU Rfree: 0.0914 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 10741 5 %RANDOM
Rwork0.1741 202486 --
obs0.1755 213227 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.91 Å2 / Biso mean: 21.5286 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.58 Å20.22 Å2
2--0.24 Å20.16 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→77.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13283 0 407 1572 15262
LS refinement shellResolution: 1.596→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 507 -
Rwork0.316 9268 -
all-9775 -
obs--59.49 %

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